rs10878983

Positions:

• chr12-69432313-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007063127.1(YEATS4):​n.859+25039G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,746 control chromosomes in the GnomAD database, including 15,408 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (15408 hom., cov: 30)
• Consequence: YEATS4 XR_007063127.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

Genes affected

YEATS4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
YEATS4	XR_007063127.1	n.859+25039G>A		intron_variant, non_coding_transcript_variant
YEATS4	XR_007063131.1	n.859+25039G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67792 AN: 151628 Hom.: 15388 Cov.: 30

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.457

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.447 AC: 67852 AN: 151746 Hom.: 15408 Cov.: 30 AF XY: 0.445 AC XY: 32996 AN XY: 74128

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.454

Alfa AF: 0.475 Hom.: 25200

Bravo AF: 0.447

Asia WGS AF: 0.417 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10878983; hg19: chr12-69826093;